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Benchmarks
Diogo Silva edited this page Jul 4, 2017
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These benchmarks were clocked with the CLI version of TriFusion for the Process module (TriSeq) on a Linux machine. The GUI version can be a bit slower.
Hardware: Intel i7-7500 @ 2.70Ghz - HD620 - NVMe SSD
| DS1 | DS2 | DS3 | DS4 | DS5 | DS6 | DS7 | DS8 | DS9 | DS10 | |
|---|---|---|---|---|---|---|---|---|---|---|
| Files | 614 | 3093 | 3093 | 3093 | 7378 | 1 | 1 | 1 | 1 | 2 |
| Taxa | 48 | 48 | 141 | 376 | 29 | 40 | 40 | 40 | 376 | 40 |
| Total bases / taxon | ~350k | 1.25M | 1.25M | 1.25M | ~601k | 4.5M | 4.5M | 4.5M | 1.25M | 9M |
| Notes | Interleave (phylip) | Interleave (nexus) | ||||||||
| Parsing | ||||||||||
| Alignment reading | 0.8 / 13.9 | 4.6 / 53.8 | 7.8 / 86.2 | 14.5 / 169.5 | 13.6 / 117.6 | 1.2 / 33.5 | 2.7 / 27.2 | 69.8 / 23.6 | 2.9 / 14.5 | 2.4 / 42.1 |
| Main operations | ||||||||||
| Conversion (nexus) | 0.5 / 0.3 | 10.4 / 0.6 | 12.2 / 0.4 | 17.0 / 0.6 | 93.7 / 1.0 | 1.0 / 69.2 | 1.0 / 65.1 | 1.0 / 73.5 | 2.4 / 22.8 | 1.5 / 69.5 |
| Conversion (interleave) | 2.4 / 0.4 | 18.1 / 0.6 | 27.7 / 0.5 | 49.9 / 0.6 | 110.1 / 1.0 | 19.1 / 51.9 | 18.9 / 56.2 | 18.8 / 56.2 | 74.9 / 17.0 | 36.8 / 52.0 |
| Concatenation | 4.7 / 5.1 | 60.1 / 20.7 | 196.6 / 21.8 | 554.4 / 21.6 | 211.2 / 7.1 | NA | NA | NA | NA | 1.7 / 34.8 |
| Secondary operations | ||||||||||
| Collapse | 0.9 / 0.3 | 9.1 / 0.2 | 11.8 / 0.5 | 15.1 / 0.4 | 56.1 / 0.1 | 1.3 / 61.2 | 1.3 / 65.7 | 1.3 / 66.3 | 3.2 / 21.1 | 2.8 / 61.5 |
| Consensus (Soft mask/ single file) | 2.3 /** 2.4** | 13.1 / 9.2 | 17.4 / 8.5 | 27.8 / 4.7 | 24.7 / 9.3 | 19.1 / 58.3 | 18.6 / 56.1 | 19.8 / 53.5 | 34.2 / 151.0 | 37.6 / 75.7 |
| Filter (Taxa contain) | 0.8 / 2.1 | 45.9 / 4.8 | 65.6 / 4.9 | 104.9 / 4.9 | 18.8 / 9.2 | NA | NA | NA | NA | 0.0 / 0.3 |
| Filter (Missing data; G50; M75) | 7.0 / 0.8 | 43.0 / 0.9 | 70.5 / 1.6 | 159.4 / 3.4 | 149.8 / 1.7 | 54.8 / 144.6 | 55.9 / 152.9 | 59.6 / 154.9 | 163.8 / 155.6 | 112.0 / 148.6 |
| Filter (Codons; 1 2) | 3.3 / 0.5 | 16.8 / 0.6 | 30.2 / 0.4 | 60.1 / 0.6 | 65.7 / 1.6 | 17.6 / 150.3 | 17.3 / 153.6 | 18.4 / 152.9 | 60.2 / 38.0 | 35.5 / 144.9 |
| Filter (Variable; 0, 200) | 2.0 / 2.2 | 55.3 / 5.2 | 75.8 / 5.4 | 128.9 / 6.5 | 10.7 / 0.9 | NA | NA | NA | NA | 0.1 / 11.4 |
| Filter (Informative; 0, 200) | 7.1 / 2.4 | 78.5 / 5.0 | 121.8 / 5.6 | 235.7 / 7.9 | 22.9 / 1.0 | NA | NA | NA | NA | 0.7 / 6.4 |
| Reverse concatenation + | ||||||||||
| Conversion (nexus) | 4.4 / 8.3 | 58.3 / 40.1 | 158.9 / 75.8 | 407.9 / 120.2 | 170.7 / 95.3 | NA | NA | NA | NA | 4.4 / 155.1 |